The Indonesian island of Java, with a surface area of 126,566 km2 and a population of 115 million people, is one of the most densely populated regions on Earth. In the Sukabumi District of West Java, the rate of Plasmodium falciparum and P. vivax malaria has increased since 1998. From October 2004 to September 2005 the Indonesian Ministry of Health and NAMRU-2 conducted a 12-month large-scale ecological study of the spatial distribution of Anopheles species in this region. The study has identified and ecologically characterized over 1600 sites and identified 15 species of Anopheles. Principal component and multiple logistic regression analyses identified ecological parameters associated with presence of nine (Anopheles aconitus, Anopheles annularis, Anopheles barbirostris, Anopheles flavirostris,Anopheles insulaeflorum, Anopheles kochi, Anopheles maculatus, Anopheles sundaicus, Anopheles vagus) of 15 Anopheles species collected. Overall, the distribution of Anopheles species in Sukabumi was found to be nonrandom and predictable on the basis of habitat characteristics. Larval ecology will be discussed in the context of land use patterns and planning of Anopheles spp. control efforts.